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galaxy.security package

Galaxy Security

class galaxy.security.Action(action, description, model)

Bases: object

__init__(action, description, model)

Initialize self. See help(type(self)) for accurate signature.

class galaxy.security.RBACAgent

Bases: object

Class that handles galaxy security

permitted_actions = <galaxy.util.bunch.Bunch object>

get_action(name, default=None)

Get a permitted action by its dict key or action name

get_actions()

Get all permitted actions as a list of Action objects

get_item_actions(action, item)

guess_derived_permissions_for_datasets(datasets=None)

can_access_dataset(roles, dataset)

can_manage_dataset(roles, dataset)

can_access_library(roles, library)

can_add_library_item(roles, item)

can_modify_library_item(roles, item)

can_manage_library_item(roles, item)

associate_components(**kwd)

create_private_user_role(user)

get_private_user_role(user)

user_set_default_permissions(user, permissions=None, history=False, dataset=False)

history_set_default_permissions(history, permissions=None, dataset=False, bypass_manage_permission=False)

set_all_dataset_permissions(dataset, permissions, new=False)

set_dataset_permission(dataset, permission)

set_all_library_permissions(trans, dataset, permissions)

set_library_item_permission(library_item, permission)

library_is_public(library)

make_library_public(library)

get_accessible_libraries(trans, user)

get_permitted_libraries(trans, user, actions)

folder_is_public(library)

make_folder_public(folder, count=0)

dataset_is_public(dataset)

make_dataset_public(dataset)

get_permissions(library_dataset)

get_all_roles(trans, cntrller)

get_legitimate_roles(trans, item, cntrller)

derive_roles_from_access(trans, item_id, cntrller, library=False, **kwd)

get_component_associations(**kwd)

components_are_associated(**kwd)

convert_permitted_action_strings(permitted_action_strings)

When getting permitted actions from an untrusted source like a form, ensure that they match our actual permitted actions.

galaxy.security.get_permitted_actions(filter=None)

Utility method to return a subset of RBACAgent’s permitted actions

Submodules

galaxy.security.idencoding module

class galaxy.security.idencoding.IdEncodingHelper(**config)

Bases: object

__init__(**config)

Initialize self. See help(type(self)) for accurate signature.

encode_id(obj_id, kind=None)

encode_dict_ids(a_dict, kind=None, skip_startswith=None)

Encode all ids in dictionary. Ids are identified by (a) an ‘id’ key or (b) a key that ends with ‘_id’

encode_all_ids(rval, recursive=False)

Encodes all integer values in the dict rval whose keys are ‘id’ or end with ‘_id’ excluding tool_id which are consumed and produced as is via the API.

decode_id(obj_id, kind=None)

encode_guid(session_key)

decode_guid(session_key)

get_new_guid()

galaxy.security.passwords module

galaxy.security.passwords.hash_password(password)

Hash a password, currently will use the PBKDF2 scheme.

galaxy.security.passwords.check_password(guess, hashed)

Check a hashed password. Supports either PBKDF2 if the hash is prefixed with that string, or sha1 otherwise.

galaxy.security.passwords.hash_password_PBKDF2(password)

galaxy.security.passwords.check_password_PBKDF2(guess, hashed)

galaxy.security.passwords.pbkdf2_bin(data, salt, iterations=100000, keylen=24, hashfunc='sha256')

Returns a binary digest for the PBKDF2 hash algorithm of data with the given salt. It iterates iterations time and produces a key of keylen bytes. By default SHA-256 is used as hash function, a different hashlib hashfunc can be provided.

galaxy.security.validate_user_input module

Utilities for validating inputs related to user objects.

The validate_* methods in this file return simple messages that do not contain user inputs - so these methods do not need to be escaped.

galaxy.security.validate_user_input.validate_email_str(email)

Validates a string containing an email address.

galaxy.security.validate_user_input.validate_password_str(password)

galaxy.security.validate_user_input.validate_publicname_str(publicname)

Validates a string containing a public username.

galaxy.security.validate_user_input.validate_email(trans, email, user=None, check_dup=True, allow_empty=False)

Validates the email format, also checks whether the domain is blocklisted in the disposable domains configuration.

galaxy.security.validate_user_input.extract_domain(email, base_only=False)

galaxy.security.validate_user_input.validate_publicname(trans, publicname, user=None)

Check that publicname respects the minimum and maximum string length, the allowed characters, and that the username is not taken already.

galaxy.security.validate_user_input.transform_publicname(publicname)

Transform publicname to respect the minimum and maximum string length, and the allowed characters. FILL_CHAR is used to extend or replace characters.

galaxy.security.validate_user_input.validate_password(trans, password, confirm)